RetrogeneDB ID: retro_fcat_480

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:71156874..71157553(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPL46
• Ensembl ID: ENSFCAG00000014966
• Aliases: None
• Description: mitochondrial ribosomal protein L46 [Source:HGNC Symbol;Acc:1192]

Sequence

>retro_fcat_480
ATGGCAGTGCCCATAAGGCAGACTCTGTTAAGGGGTGGCGAATGACTGGTAGCAGTTTGAGGGGCTCTGGGCCGGAGCCT
GGATTCTCTTGGCCTTACTGTTGTGGCCTCATCTTGGAGCAGTGGGTCTCTGTAGCACCTGTTGCACATGTTGTGCCTAC
AGCAGCTGCCGGTGGCCTCCAGTTGGCCTCTAAGCCACAGAAAGAGATGACGGTCTCTATTACAAAAGATCAAGATGGAG
AGAGTTTGCATTCAGACCATGAGCCTGGTACTTTGGATCAAGCCTAGTGACCAGCAAAGAAGAAAGCTGACTTCCATGAT
GAAGAGGAACAGAATATACTGCTGGTGTAGGATTTGGAAGATATATGGGAGCAGAAAGTTTTACCCTTCAAACCTGGAGC
TCACATTCCAGAAGCTGATAAAAAGAATGACCAAATCTCACTGCACCAAAAAATGGGCAGGAACCTTGTTCTGCTGGTCA
AAGAGAAGCTTGGAGATCAGGATGTTTGGATACTCCTACAGGAAGAGTGGCAACCCAGGGAGACCTTCTGAGGAACAGCT
GAGTGAATACTGGCCACACTCTCAGAAAAGGACATGGAAGCCAAGTCCCTGGCAATTGTACCCTGTGGCCACTACAAGTT
CAATTCCCTCAGGCCATGCAGACAAAGTAGGCTCAGGGC

Alignment

ORF - retro_fcat_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.23 %
• Parental protein coverage: 81.49 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAPVRRTLLQA-AKGWRRFEGHWAG-SLGSRSLAPAAAPLSSGSPWRLVGALCLQRPPLVSKPLTPLQE
          MA.P.R.TLL...A..W..FEG.WAG.SL.S..L...A...SSGS...L...LCLQ..P..S........
Retrocopy MAVPIRQTLLRG>ANDW*QFEGLWAG<SLDSLGLTVVASSWSSGSL*HLLHMLCLQQLPVASSWPLSHRK

Parental  EMAALLQQIEVER-SMYSDHELRALDEAQRLAKRKADLYDEEEDEQNVLLVQDLEDVWEQKFLQFKPGAR
          ....LLQ.I..ER.S..SDHE...LD.A...AK.KAD..DEEE..QN.LLV.DLED.WEQK.L.FKPGA.
Retrocopy R*RSLLQKIKMER<SLHSDHEPGTLDQA**PAKKKADFHDEEE--QNILLV*DLEDIWEQKVLPFKPGAH

Parental  ITEADEKNDRTSLHRKLDRNLVLLVKEKLGDKDVWILPQAEWQPGETLRGTAERTLATLSEKKVEAKFLG
          I.EAD.KND..SLH.K..RNLVLLVKEKLGD.DVWIL.Q.EWQP.ET..GTAE..LATLSEK..EAK.L.
Retrocopy IPEADKKNDQISLHQKMGRNLVLLVKEKLGDQDVWILLQEEWQPRETF*GTAE*ILATLSEKDMEAKSLA

Parental  NAPCGHYKF-KFPQAMRTESSLG
          ..PCGHYKF..FPQAM.T....G
Retrocopy IVPCGHYKF<QFPQAMQTK*AQG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	8.38 RPM
SRP017611_kidney	0.00 RPM	13.19 RPM
SRP017611_liver	0.00 RPM	8.59 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_480 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_480 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013019	1 retrocopy	retro_cjac_3018,
Felis catus	ENSFCAG00000014966	1 retrocopy	retro_fcat_480 ,
Microcebus murinus	ENSMICG00000015826	1 retrocopy	retro_mmur_741,
Otolemur garnettii	ENSOGAG00000004736	1 retrocopy	retro_ogar_1280,
Rattus norvegicus	ENSRNOG00000018547	1 retrocopy	retro_rnor_433,